emeyerlab / ipdtools Goto Github PK

Building and emplacement of tree_predict.c to tree_predict.so works well on Ubuntu 18 LTS x86. However it won't work on Windows or MacOS.

There is not a lot of work to do but as I don't have access to any MacOS or Windows I can't really do it.
EDIT: Also a compatibility issue, maybe, for the new ARM-based MacOS

The temporary files are not always cleaned properly

The IPD modelling (especially on last version of chemistries) is not very well benchmarked and PacBio's data are not easily available.

It would be great to benchmark it on real world data (Whole Genome amplified VS known methylation):

• On long inserts (~ >1000 bp)
• On short inserts (~ 150-250 bp)

Data published by J. Beaulaurier et Al might help on that

https://www.ncbi.nlm.nih.gov/pubmed/29227468

https://www.nature.com/articles/ncomms8438

This would allow to access Sensibility and specificity of the in silico model compared to the WGA